A novel pathway-based approach improves lung cancer risk prediction using germline genetic variations

Cancer Epidemiology Biomarkers and Prevention

Volumn 25, Issue 8, 2016, Pages 1208-1215

  Qian, David C ^a   Han, Younghun ^a   Byun, Jinyoung ^a   Shin, Hae Ri ^a   Hung, Rayjean J ^b   McLaughlin, John R ^c   Landi, Maria Teresa ^d   Seminara, Daniela ^d   Amos, Christopher I ^a  

^a DARTMOUTH MEDICAL SCHOOL   (United States)

^b MOUNT SINAI HOSPITAL   (Canada)

^c UNIVERSITY OF TORONTO   (Canada)

^d NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; AGED; ARTICLE; CANCER RISK; COLORECTAL CANCER; CONTROLLED STUDY; FEMALE; GENE FREQUENCY; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GENETIC VARIATION; GENOTYPE; HUMAN; LUNG; LUNG CANCER; MAJOR CLINICAL STUDY; MALE; MIDDLE AGED; OVARY CANCER; PREDICTION; PRIORITY JOURNAL; PROSTATE; SINGLE NUCLEOTIDE POLYMORPHISM; SMOKING; CASE CONTROL STUDY; EPIDEMIOLOGY; GENETIC PREDISPOSITION; GENETICS; LUNG TUMOR; ODDS RATIO; RECEIVER OPERATING CHARACTERISTIC; RISK FACTOR; VERY ELDERLY;

AGED; AGED, 80 AND OVER; CASE-CONTROL STUDIES; FEMALE; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; HUMANS; LUNG NEOPLASMS; MALE; MIDDLE AGED; ODDS RATIO; POLYMORPHISM, SINGLE NUCLEOTIDE; RISK FACTORS; ROC CURVE; SMOKING;

EID: 84982899884     PISSN: 10559965     EISSN: None     Source Type: Journal    
DOI: 10.1158/1055-9965.EPI-15-1318     Document Type: Article

References (51)

1. Fitzmaurice C, Dicker D, Pain A, Hamavid H, Moradi-Lakeh M, MacIntyre MF, et al. The global burden of cancer 2013. JAMA Oncol 2015;1:505-27.
2. National Cancer Institute. SEER Stat Fact Sheets: Lung and Bronchus Cancer. Bethesda, MD: National Cancer Institute; 2015.
3. The National Lung Screening Trial Research Team, Aberle DR, Adams AM, Berg CD, Black WC, Clapp JD, et al. Reduced lung-cancermortality with lowdose computed tomographic screening. N Engl J Med 2011;365:395-409.
4. Humphrey L, Deffebach M, Pappas M, Baumann C, Artis K, Priest Mitchell J, et al. Screening for lung cancer: systematic review to update the U.S. Preventive Services Task Force recommendation. Evidence synthesis no. 105. Rockville, MD: Agency for Healthcare Research and Quality; 2013.
5. Chen X, Gorlov IP, Ying J, Merriman KW, Kimmel M, Lu C, et al. Initial medical attention on patients with early-stage non-small cell lung cancer. PLoS One 2012;7:e32644.
6. Field JK, Chen Y, Marcus MW, McRonald FE, Raji OY, Duffy SW. The contribution of risk prediction models to early detection of lung cancer. J Surg Oncol 2013;108:304-11.
7. Wang X, Oldani MJ, Zhao X, Huang X, Qian D. A review of cancer risk prediction models with genetic variants. Cancer Inform 2014;13:19-28.
8. Bach PB, Kattan MW, Thornquist MD, Kris MG, Tate RC, Barnett MJ, et al. Variations in lung cancer risk among smokers. J Natl Cancer Inst 2003;95:470-8.
9. Spitz MR, Hong WK, Amos CI, Wu X, Schabath MB, Dong Q, et al. A risk model for prediction of lung cancer. J Natl Cancer Inst 2007;99:715-26.
10. Cassidy A, Myles JP, van Tongeren M, Page RD, Liloglou T, Duffy SW, et al. The LLP risk model: an individual risk prediction model for lung cancer. Br J Cancer 2008;98:270-6.
11. Tammemagi CM, Pinsky PF, Caporaso NE, Kvale PA, Hocking WG, Church TR, et al. Lung cancer risk prediction: prostate, lung, colorectal and ovarian cancer screening trial models and validation. J Natl Cancer Inst 2011;103: 1058-68.
12. Hoggart C, Brennan P, Tjonneland A, Vogel U, Overvad K, Ostergaard JN, et al. A risk model for lung cancer incidence. Cancer Prev Res 2012;5:834-46.
13. Raji OY, Agbaje OF, Duffy SW, Cassidy A, Field JK. Incorporation of a genetic factor into an epidemiologic model for prediction of individual risk of lung cancer: the Liverpool Lung Project. Cancer Prev Res 2010;3:664-9.
14. Spitz MR, Amos CI, Land S, Wu X, Dong Q, Wenzlaff AS, et al. Role of selected genetic variants in lung cancer risk in African Americans. J Thorac Oncol 2013;8:391-7.
15. Weissfeld JL, Lin Y, Lin HM, Kurland BF, Wilson DO, Fuhrman CR, et al. Lung cancer risk prediction using common SNPs located in GWAS-identified susceptibility regions. J Thorac Oncol 2015:10;1538-45.
16. Li H, Yang L, Zhao X, Wang J, Qian J, Chen H, et al. Prediction of lung cancer risk in a Chinese population using a multifactorial genetic model. BMC Med Genet 2012;13:118.
17. Timofeeva MN, Hung RJ, Rafnar T, Christiani DC, Field JK, Bickeboller H, et al. Influence of common genetic variation on lung cancer risk: meta-analysis of 14 900 cases and 29 485 controls. Hum Mol Genet 2012;21:4980-95.
18. Amos CI, Wu X, Broderick P, Gorlov IP, Gu J, Eisen T, et al. Genome-wide association scan of tag SNPs identifies a susceptibility locus for lung cancer at 15q25.1. Nat Genet 2008;40:616-22.
19. Wang Y, Broderick P, Webb E, Wu X, Vijayakrishnan J, Matakidou A, et al. Common 5p15.33 and 6p21.33 variants influence lung cancer risk. Nat Genet 2008;40:1407-9.
20. Eisen T, Matakidou A, Houlston R, GELCAPS Consortium. Identification of low penetrance alleles for lung cancer: the GEnetic Lung CAncer Predisposition Study (GELCAPS). BMC Cancer 2008;8:244.
21. Power C, Elliott J. Cohort profile: 1958 British birth cohort (National Child Development Study). Int J Epidemiol 2006;35:34-41.
22. Hung RJ, McKay JD, Gaborieau V, Boffetta P, Hashibe M, Zaridze D, et al. A susceptibility locus for lung cancer maps to nicotinic acetylcholine receptor subunit genes on 15q25. Nature 2008;452:633-7.
23. Scelo G, Constantinescu V, Csiki I, Zaridze D, Szeszenia-Dabrowska N, Rudnai P, et al. Occupational exposure to vinyl chloride, acrylonitrile and styrene and lung cancer risk (Europe). Cancer Causes Control 2004;15: 445-52.
24. Sauter W, Rosenberger A, Beckmann L, Kropp S, Mittelstrass K, Timofeeva M, et al. Matrix metalloproteinase 1 (MMP1) is associated with early-onset lung cancer. Cancer Epidemiol Biomarkers Prev 2008;17:1127-35.
25. Thorgeirsson TE, Geller F, Sulem P, Rafnar T, Wiste A, Magnusson KP, et al. A variant associated with nicotine dependence, lung cancer and peripheral arterial disease. Nature 2008;452:638-42.
26. Yang J, Ferreira T, Morris AP, Medland SE Genetic Investigation of ANthropometric Traits (GIANT) Consortium, DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium, et al. Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits. Nat Genet 2012;44:369-75.
27. Landi MT, Consonni D, Rotunno M, Bergen AW, Goldstein AM, Lubin JH, et al. Environment And Genetics in Lung cancer Etiology (EAGLE) study: an integrative population-based case-control study of lung cancer. BMC Public Health 2008;8:203.
28. Hayes RB, Sigurdson A, Moore L, Peters U, Huang WY, Pinsky P, et al. Methods for etiologic and early marker investigations in the PLCO trial. Mutat Res 2005;592:147-54.
29. Delaneau O, Marchini J. The 1000 Genomes Project Consortium. Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel. Nat Commun 2014;5:3934.
30. Delaneau O, Marchini J, Zagury JF. A linear complexity phasingmethod for thousands of genomes. Nat Methods 2012;9:179-81.
31. Howie BN, Donnelly P, Marchini J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet 2009;5:e1000529.
32. Wang Y, McKay JD, Rafnar T, Wang Z, Timofeeva MN, Broderick P, et al. Rare variants of large effect in BRCA2 and CHEK2 affect risk of lung cancer. Nat Genet 2014;46:736-41.
33. DeLong ER, DeLong DM, Clarke-Pearson DL. Comparing the areas under two or more correlated receiver operating characteristic curves: a nonparametric approach. Biometrics 1988;44:837-45.
34. Yang J, Lee SH, Goddard ME, Visscher PM. GCTA: a tool for genome-wide complex trait analysis. Am J Hum Genet 2011;88:76-82.
35. The GTEx Consortium. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science 2015;348:648-60.
36. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci 2005;102:15545-50.
37. Pencina MJ, D'Agostino RB, Steyerberg EW. Extensions of net reclassification improvement calculations to measure usefulness of new biomarkers. Stat Med 2011;30:11-21.
38. Cohen J. A coefficient of agreement for nominal scales. Educ Psychol Meas 1960;20:37-46.
39. Van der Weele TJ, Asomaning K, Tchetgen Tchetgen EJ, Han Y, Spitz MR, Shete S, et al. Genetic variants on 15q25.1, smoking, and lung cancer: an assessment of mediation and interaction. Am J Epidemiol 2012;175: 1013-20.
40. Rudd MF, Webb EL, Matakidou A, Sellick GS, Williams RD, Bridle H, et al. Variants in the GH-IGF axis confer susceptibility to lung cancer. Genome Res 2006;16:693-701.
41. Xun X, Wang H, Yang H, Wang H, Wang B, Kang L, et al. CLPTM1L genetic polymorphisms and interaction with smoking and alcohol drinking in lung cancer risk: a case-control study in the Han population from northwest China. Medicine 2014;93:e289.
42. Leening MJ, Vedder MM, Witteman JC, Pencina MJ, Steyerberg EW. Net reclassification improvement: computation, interpretation, and controversies: a literature review and clinician's guide. Ann Intern Med 2014;160: 122-31.
43. Li K, Husing A, Sookthai D, Bergmann M, Boeing H, Becker N, et al. Selecting high-risk individuals for lung cancer screening: a prospective evaluation of existing risk models and eligibility criteria in the German EPIC cohort. Cancer Prev Res 2015;8:777-85.
44. Wray NR, Yang J, Hayes BJ, Price AL, Goddard ME, Visscher PM. Pitfalls of predicting complex traits from SNPs. Nat Rev Genet 2013; 14:507-15.
45. Maier R, Moser G, Chen GB, Ripke S, Cross-Disorder Working Group of the Psychiatric Genomics Consortium, Coryell W, et al. Joint analysis of psychiatric disorders increases accuracy of risk prediction for schizophrenia, bipolar disorder, and major depressive disorder. Am J Hum Genet 2015;96:283-94.
46. Guo G, Zhao F, Wang Y, Zhang Y, Du L, Su G. Comparison of single-trait and multiple-trait genomic prediction models. BMC Genet 2014;15:30.
47. Tammemagi MC, Katki HA, Hocking WG, Church TR, Caporaso N, Kvale PA, et al. Selection criteria for lung-cancer screening. N Engl J Med 2013;368:728-36.
48. Sakamaki A, Katsuragi Y, Otsuka K, Tomita M, Obata M, Iwasaki T, et al. Bcl11b SWI/SNF-complex subunit modulates intestinal adenoma and regeneration after gamma-irradiation through Wnt/beta-catenin pathway. Carcinogenesis 2015;36:622-31.
49. Korc M. Smad4: gatekeeper gene in head and neck squamous cell carcinoma. J Clin Invest 2009;119:3208-11.
50. Samet JM, Avila-Tang E, Boffetta P, Hannan LM, Olivo-Marston S, Thun MJ, et al. Lung cancer in never smokers: clinical epidemiology and environmental risk factors. Clin Cancer Res 2009;15:5626-45.
51. Devesa SS, Bray F, Vizcaino AP, Parkin DM. International lung cancer trends by histologic type: male:female differences diminishing and adenocarcinoma rates rising. Int J Cancer 2005;117:294-9.